Tom Tango, et al wrote a book (called "The Book") and there is a chapter on line-ups. It's not based on simply looking at batting average or OBP. It's based on a complex algorithm which estimates the number of runs that a player will contribute to in each batting order position.
He didn't say the best hitter bats second on every team. He was saying that all things being equal, it is better for the average team to bat their best hitter second than to have him hitting third. There is nothing special about the number three spot which makes it advatageous to always put you best hitter there. It doesn't alway work for the best hitter to bat second either. It's just that if you are going to pick a spot for your best hitter without considering anything else, the second spot would have the edge.
Torres does not always bat second. Sometimes he bats first or third. Hinch has a different line-up every night based on matchups.